Abstract

Genome-wide CRISPR-cas9 screening have been performed at a large scale using human cancer 2D cell lines to identify new drug targets that may help in the development of new therapies. Patient-derived cancer organoids recapitulate genomic and transcriptomic heterogeneity of the original lesion, allowing investigations to study different components of cancer biology more closely related to patients. Here, we performed genome-wide CRISPR-cas9 screens in 55 human cancer organoids from 3 different cancer types, with colorectal cancer as the most represented cohort (n=41). To enable this work, organoid cultures were grown in suspension with 5% BME, with results showing that organoids grown in these conditions are genomically and phenotypically indistinguishable from organoids grown using conventional methods. In addition, we used a minimal genome-wide CRISPR-Cas9 library that uses inly 2 optimised sgRNA per gene, as compared to 5 sgRNA contained in a previously designed library (Project Score). This minimal library, which is 42% smaller that most genome-wide libraries, retains specificity and sensitivity to identify gene dependencies, when compared to the original library. Analysis of the results recapitulates cancer dependencies previously described in cell lines, such as the addiction of microsatellite instability cancers to the Werner syndrome ATP-dependent helicase. In addition, we observe dependencies with clinical implications only observed in organoids. This study demonstrates the utility of large-scale perturbation screens in cancer organoids as a tool for cancer drug discovery.